Still, such denunciations were far from unanimous in the state. A prominent New Mexico Republican, Gavin Clarkson, a former Trump administration official who is now running for United States Senate, met with masked members of the group in March and praised their efforts, according to a video of the encounter uploaded to Facebook.
But Mr. Clarkson said on Twitter on Saturday that he condemned militia activities. “Masked militiamen are the antithesis of what a free republic looks like,” he said.
Jim Benvie, a spokesman for the militia, did not immediately respond to requests for comment about the arrest of Mr. Hopkins.
The F.B.I. said in a statement that the police department of Sunland Park, N.M., had assisted with the arrest. Mr. Hopkins, 69, is scheduled to appear on Monday in Federal District Court in Las Cruces, N.M.
Mr. Hopkins, whose residence is in Flora Vista in northwest New Mexico, had already come under the scrutiny of groups tracking right-wing militias around the United States. He was convicted in 2006 for impersonating an officer and for felony firearm possession, according to The Daily Beast.
Despite the recent criticism over its operations in New Mexico, the militia led by Mr. Hopkins maintains a wide reach on Facebook and YouTube.
Speaking to someone using a voice distorter while wearing a gas mask, Mr. Hopkins appeared on a right-wing extremist YouTube channel in November. He claimed to be in touch with President Trump after a chance meeting at a Las Vegas casino.